Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

High Abundance of Ammonia-Oxidizing Archaea in Coastal Waters, Determined Using a Modified DNA Extraction Method

(2010) H. Urakawa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight

(2010) J. Michael Beman et al.   ENVIRONMENTAL MICROBIOLOGY

Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context

(2010) Rita Bartossek et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

(2010) James T Hollibaugh et al.   ISME Journal

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate

(2010) Maria Vila-Costa et al.   ISME Journal

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

(2010) Torsten Thomas et al.   ISME Journal

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Cyclodepsipeptides from Marine Sponges: Natural Agents for Drug Research

(2010) Gowri Shankar Bagavananthem Andavan et al.   Marine Drugs

Database resources of the National Center for Biotechnology Information

(2010) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

(2010) S. Lucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abundance of Ammonia-Oxidizing Archaea and Bacteria along an Estuarine Salinity Gradient in Relation to Potential Nitrification Rates

(2009) A. E. Bernhard et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility

(2009) K. Stoecker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

(2009) Rachel S. Poretsky et al.   ENVIRONMENTAL MICROBIOLOGY

Complex nitrogen cycling in the spongeGeodia barretti

(2009) Friederike Hoffmann et al.   ENVIRONMENTAL MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

(2008) Annika C. Mosier et al.   ENVIRONMENTAL MICROBIOLOGY

Physiology, phylogeny andin situevidence for bacterial and archaeal nitrifiers in the marine spongeAplysina aerophoba

(2008) Kristina Bayer et al.   ENVIRONMENTAL MICROBIOLOGY

Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium ‘CandidatusNitrospira defluvii’

(2008) Frank Maixner et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges

(2008) Doris Steger et al.   ENVIRONMENTAL MICROBIOLOGY

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

(2008) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA